Methods and compositions for treatment of ocular disorders and blinding diseases

ABSTRACT

Codon optimized nucleic acid sequences for the long form and short form of RdCVF are provided, as well as recombinant viral vectors, such as AAV, expression cassettes, proviral plasmids or other plasmids containing the codon optimized sequences. Recombinant vectors are provided that express the codon optimized RdCVFL and RdCVF individually, or express two copies of a codon optimized RdCVF or RdCVFL nucleic acid sequence, or both RdCVFL and RdCVF in a single vector or virus. Compositions containing these codon optimized sequences are useful in methods for treating, retarding or halting certain blinding diseases resulting from the absence or inappropriate expression of RdCVF and RdCVFL.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a national stage of International Patent Application No. PCT/US2017/012277, filed Jan. 5, 2017, which claims the benefit of the priority of U.S. Provisional Patent Application No. 62/275,006, filed Jan. 5, 2016, which applications are incorporated herein by reference.

INCORPORATION-BY-REFERENCE OF MATERIAL SUBMITTED IN ELECTRONIC FORM

Applicant hereby incorporates by reference the Sequence Listing material filed in electronic form herewith. This file is labeled “15-7572PCT_SEQ_List_ST25.txt” and dated Jan. 4, 2017.

BACKGROUND OF THE INVENTION

Rod-cone dystrophies, such as retinitis pigmentosa (RP), are genetically heterogeneous retinal degenerative diseases characterized by the progressive death of rod photoreceptors, followed by the consecutive loss of cones. RP patients initially present with loss of vision under dim-light conditions as a result of rod dysfunction, with relative preservation of macular cone-mediated vision. As the disease progresses, however, the primary loss of rods is followed by cone degeneration and a deficit in corresponding cone-mediated vision. Retention of cone-mediated sight in RP patients would lead to a significant improvement in their quality of life.

A variety of methods for treatment of such diseases have involved a protein, termed RdCVF, which is differentially transcribed and expressed in subjects suffering from retinal dystrophies, including age-related macular degeneration. The long (RdCVFL) and short (RdCVF) forms produced by alternative splicing of the NXNL1 gene have been identified in humans and other mammals. See, e.g., US Patent Application Publication No. US2009/0062188; Byrne et al “Viral-mediated RdCVF and RdCVFL expression protects cone and rod photoreceptors in retinal degeneration”, January 2015, J. Clin. Invest., 125(1):105-116.

No currently approved treatment for retinal degenerations exists other than one treatment which involves oral administration of high dose vitamin A. That treatment, however, is controversial and now that we know more about the retinoid cycle in retinal degenerations, is, in fact, likely to worsen retinal degeneration in many genetic forms of retinal disease.

A continuing need in the art therefore exists for new and effective tools to facilitate treatment of ocular diseases such as retinal degenerations, RP, macular degeneration, and other rod-cone dystrophies and retinal degenerative diseases.

SUMMARY OF THE INVENTION

In one aspect, a codon optimized cDNA sequence SEQ ID NO: 1 encoding human RdCVFL long form or a codon optimized cDNA sequence SEQ ID NO: 2 encoding RdCVF short form is provided.

In another aspect an expression cassette comprises a codon optimized nucleic acid sequence SEQ ID NO: 1 that encodes RdCVFL or a codon optimized nucleic acid sequence SEQ ID NO: 2 that encodes RdCVF, or both a codon optimized nucleic acid sequence SEQ ID NO: 2 that encodes RdCVF and a codon optimized nucleic acid sequence SEQ ID NO: 1 that encodes RdCVFL, or two copies of a codon optimized nucleic acid sequence SEQ ID NO: 2 that encodes RdCVF, or two copies of a codon optimized nucleic acid sequence SEQ ID NO: 1 that encodes RdCVFL. In still other embodiments, the expression cassette is positioned between 5′ and 3′ AAV ITR sequences, then referred to as an rAAV genome.

In another aspect, a vector is provided that contains one or more of the expression cassettes described herein and host cells containing the vectors or expression cassettes are provided.

In another aspect, a proviral plasmid comprises sequences encoding an AAV capsid and an recombinant AAV genome that comprises AAV inverted terminal repeat sequences and an expression cassette comprising the codon optimized nucleic acid sequence(s) that encodes RdCVFL, RdCVF-S, both RdCVFL and RdCVF, two copies of RdCVF, or two copies of RdCVFL, and expression control sequences that direct expression of the encoded protein(s) in a host cell. In certain embodiments, the AAV genome is modular.

In another embodiment, a recombinant adeno-associated virus (AAV) comprises an AAV capsid and an recombinant AAV genome that comprises AAV inverted terminal repeat sequences and an expression cassette comprising a codon optimized nucleic acid sequence that encodes RdCVFL, RdCVF, both RdCVF and RdCVFL, or two copies of RdCVF or two copies of RdCVFL, and expression control sequences that direct expression of the encoded protein(s) in a host cell.

In yet a further aspect a pharmaceutical composition comprises a pharmaceutically acceptable carrier, diluent, excipient and/or adjuvant and the nucleic acid sequence, a plasmid, a vector, or a viral vector, such as the rAAV, described specifically herein.

In another aspect, a method for treating, retarding or halting progression of blindness in a mammalian subject comprises administering the compositions described herein containing a codon optimized cDNA sequence encoding human RdCVFL long form or RdCVF short form, or both forms of RdCVF or multiple copies of the short or long form.

In yet a further aspect, a method of generating a recombinant rAAV comprises culturing a packaging cell carrying a plasmid or proviral plasmid containing the codon optimized cDNA sequence encoding human RdCVFL long form or RdCVF short form, or both forms of RdCVF or multiple copies of the short or long form, in the presence of sufficient viral sequences to permit packaging of the AAV viral genome into an infectious AAV envelope or capsid.

Still other aspects and advantages of these compositions and methods are described further in the following detailed description of the preferred embodiments thereof.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 (SEQ ID NO: 1) is a human codon optimized DNA sequence encoding RdCVFL with N-terminal SfiI and Kozak and C-terminal BglII restrictions sites added for cloning. Nucleotides 23-655 of SEQ ID NO: 1 represent the sequence of codon optimized RdCVFL. The restriction sites are represented by italicized and lower case lettering at nucleotides 1-22 and 656-665 of SEQ ID NO: 1.

FIG. 2 (SEQ ID NO: 2) is a human codon optimized DNA sequence encoding RdCVF with N-terminal NotI and Kozak and C-terminal MI restrictions sites added for cloning. Nucleotides 16-339 of SEQ ID NO: 2 represent the sequence of codon optimized RdCVF (short form). The restriction sites are represented by italicized and lower case lettering at nucleotides 1-15 and 340-348 of SEQ ID NO: 2.

FIG. 3 is the alignment of the long form of optimized RdCVFL (Nucleotides 23-655 of SEQ ID NO: 1 with an added 5′ ATG codon) with the long form of native RdCVF SEQ ID NO: 3. Identities are 531/636 (83%). SEQ ID NO: 3 is the 636 nucleotide sequence of the native nucleic acid sequence encoding the long form of Homo sapiens nucleoredoxin-like 1 (NXNL1), including a start codon ATG at positions 1-3. Nucleotides 1-327 of SEQ ID NO: 3 are the short form of native RdCVF. The long form gene sequence is also reported at GenBank accession No. NM_138454.1.

FIG. 4 illustrates the alignment of the short form of optimized RdCVF (nucleotides 16-339 of SEQ ID NO: 2 with an added 5′ ATG codon) with the short form of native RdCVF (nucleotides 1 to 327 of SEQ ID NO: 3). Identities are 271/327 (83%).

FIG. 5 is a schematic map of a single rAAV genome which contains between a 5′ ITR and 3′ITR, an expression cassette containing tandem transgenes, i.e., the first transgene containing sequences (including a promoter and poly A sequence) necessary for expression of a codon optimized short form of RdCVF (optRdCVF) and the second transgene containing sequences (including a promoter and poly A sequence) necessary for expression of a codon optimized long form of RdCVFL (optRdCVFL).

FIG. 6A is a schematic map of a single rAAV genome which contains between a 5′ ITR and 3′ITR, an expression cassette containing tandem transgenes, i.e., the first transgene containing sequences (including a promoter and poly A sequence) necessary for expression of a codon optimized short form of RdCVF (optRdCVF) and the second transgene containing sequences (including a promoter and poly A sequence) necessary for expression of a second copy of the codon optimized short form of RdCVF (optRdCVF). This rAAV genome is referred to as 2xRdCVF.

FIG. 6B is a more detailed map of the same rAAV genome of FIG. 6A.

DETAILED DESCRIPTION

The methods and compositions described herein involve compositions and methods for delivering optimized human rod-cone variability factors (hRdCVF) to mammalian subjects for the treatment of ocular disorders, primarily blinding diseases such as rod-cone dystrophies. The compositions and methods described herein involve expression cassettes, vectors, recombinant viruses and other compositions for delivery of multiple, different versions of the hRdCVF. Such compositions involve both codon optimization and the assembly of multiple, different versions of the hRdCVF, i.e., both the long and short forms or multiple copies of the same versions of RdCVF (multiple short or multiple long forms) in the same expression cassette, i.e., as tandem transgenes flanked by a single pair of ITR sequences within the same AAV genome, or vector or virus. These features not only increase the efficacy of the product but also, since a lower dose of reagent is used, increase safety. It is anticipated that this optimization of the transgene cassette could theoretically maximize the level of production of the experimental protein compared to levels that can be generated using the endogenous sequence.

The compositions and methods described herein, in one embodiment, are useful to prevent degeneration of cone photoreceptors in different genetic forms of retinal degeneration or in degenerative changes associated with other multi-systemic diseases (for example, diabetic retinopathy in diabetes).

Technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs and by reference to published texts, which provide one skilled in the art with a general guide to many of the terms used in the present application. The definitions contained in this specification are provided for clarity in describing the components and compositions herein and are not intended to limit the claimed invention.

NXNL1 is a member of the family rod-cone variability factor genes genes involved in a number of ocular diseases. This gene encodes for a long form, RdCVFL and a short form, RdCVF. The native nucleic acid sequence encoding human RdCVF, e.g., Homo sapiens nucleoredoxin-like 1 (NXNL1), is shown in SEQ ID NO: 3. See also GenBank accession No. NM_138454.1. See, also U.S. Pat. Nos. 7,795,387; 8,114,849, 8,394,756, as well as related patent disclosures, incorporated by reference for additional disclosure of this protein family. The short form of RdCVF is nucleotides 1-327 of SEQ ID NO: 3.

In certain embodiments of this invention, a subject has an “ocular disorder”, for which the components, compositions and methods of this invention are designed to treat. As used herein, the term “subject” as used herein means a mammalian animal, including a human, a veterinary or farm animal, a domestic animal or pet, and animals normally used for clinical research. In one embodiment, the subject of these methods and compositions is a human. Still other suitable subjects include, without limitation, murine, rat, canine, feline, porcine, bovine, ovine, and others. As used herein, the term “subject” is used interchangeably with “patient”.

As used herein “ocular disorder” includes, rod-cone dystrophies and retinal diseases including, without limitation, Stargardt disease (autosomal dominant or autosomal recessive), retinitis pigmentosa, age-related macular degeneration, rod-cone dystrophy, Leber's congenital amaurosis, Usher's syndrome, Bardet-Biedl Syndrome, Best disease, Bassen-Kornzweig syndrome, retinoschisis, untreated retinal detachment, pattern dystrophy, achromatopsia, choroideremia, ocular albinism, enhanced S cone syndrome, diabetic retinopathy, retinopathy of prematurity, sickle cell retinopathy, refsun syndrome, Congenital Stationary Night Blindness, glaucoma, gyrate atrophy or retinal vein occlusion. In another embodiment, the subject has, or is at risk of developing glaucoma, Leber's hereditary optic neuropathy, lysosomal storage disorder, or peroxisomal disorder. Clinical signs of such ocular diseases include, but are not limited to, decreased peripheral vision, decreased central (reading) vision, decreased night vision, loss of color perception, reduction in visual acuity, decreased photoreceptor function, pigmentary changes, and ultimately blindness.

As used herein, the term “treatment” or “treating” is defined encompassing administering to a subject one or more compounds or compositions described herein for the purposes of amelioration of one or more symptoms of an ocular disease. “Treatment” can thus include one or more of reducing onset or progression of an ocular disease, preventing disease, reducing the severity of the disease symptoms, or retarding their progression, including the progression of blindness, removing the disease symptoms, delaying onset of disease or monitoring progression of disease or efficacy of therapy in a given subject.

The term “exogenous” as used to describe a nucleic acid sequence or protein means that the nucleic acid or protein does not naturally occur in the position in which it exists in a chromosome, recombinant plasmid, vector or host cell. An exogenous nucleic acid sequence also refers to a sequence derived from and inserted into the same host cell or subject, but which is present in a non-natural state, e.g. a different copy number, or under the control of different regulatory elements.

The term “heterologous” as used to describe a nucleic acid sequence or protein means that the nucleic acid or protein was derived from a different organism or a different species of the same organism than the host cell or subject in which it is expressed. The term “heterologous” when used with reference to a protein or a nucleic acid in a plasmid, expression cassette, or vector, indicates that the protein or the nucleic acid is present with another sequence or subsequence which with which the protein or nucleic acid in question is not found in the same relationship to each other in nature.

The terms “percent (%) identity”, “sequence identity”, “percent sequence identity”, or “percent identical” in the context of nucleic acid sequences refers to the bases in the two sequences which are the same when aligned for correspondence. The percent identity is determined by comparing two sequences aligned under optimal conditions over the sequences to be compared. The length of sequence identity comparison may be over the full-length of the RdCVF and RdCVFL coding sequence, or a fragment of at least about 100 to 150 nucleotides, or as desired. However, identity among smaller fragments, e.g. of at least about nine nucleotides, usually at least about 20 to 24 nucleotides, at least about 28 to 32 nucleotides, at least about 36 or more nucleotides, may also be desired. Multiple sequence alignment programs are also available for nucleic acid sequences. Examples of such programs include, “Clustal W”, “CAP Sequence Assembly”, “BLAST”, “MAP”, and “MEME”, which are accessible through Web Servers on the internet. Other sources for such programs are known to those of skill in the art. Alternatively, Vector NTI utilities are also used. There are also a number of algorithms known in the art that can be used to measure nucleotide sequence identity, including those contained in the programs described above. As another example, polynucleotide sequences can be compared using Fasta™, a program in GCG Version 6.1. Commonly available sequence analysis software, more specifically, BLAST or analysis tools provided by public databases may also be used.

The term “isolated” means that the material is removed from its original environment (e.g., the natural environment if it is naturally occurring). For example, a naturally-occurring polynucleotide or polypeptide present in a living animal is not isolated, but the same polynucleotide or polypeptide, separated from some or all of the coexisting materials in the natural system, is isolated, even if subsequently reintroduced into the natural system. Such polynucleotides could be part of a vector and/or such polynucleotides or polypeptides could be part of a composition, and still be isolated in that such vector or composition is not part of its natural environment.

By “engineered” is meant that the nucleic acid sequences encoding the RdCVF (short form) and RdCVFL (long form) proteins described herein are assembled and placed into any suitable genetic element, e.g., naked DNA, phage, transposon, cosmid, episome, etc., which transfers the RdCVF sequences carried thereon to a host cell, e.g., for generating non-viral delivery systems (e.g., RNA-based systems, naked DNA, or the like) or for generating viral vectors in a packaging host cell and/or for delivery to a host cells in a subject. In one embodiment, the genetic element is a plasmid. The methods used to make such engineered constructs are known to those with skill in nucleic acid manipulation and include genetic engineering, recombinant engineering, and synthetic techniques. See, e.g., Green and Sambrook, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, Cold Spring Harbor, N.Y. (2012). The teachings of this specification coupled with known techniques permits one of skill in the art to reproduce the exemplified

The term “transgene” as used herein means an exogenous or engineered protein-encoding nucleic acid sequence that is under the control of a promoter or expression control sequence in an expression cassette, rAAV genome, recombinant plasmid or proviral plasmid, vector, or host cell described in this specification. In certain embodiments, the transgene is a codon optimized RdCVFL encoding sequence SEQ ID NO: 1. In certain embodiments, the transgene is a codon optimized RdCVF (short form) encoding sequence SEQ ID NO:2. In other embodiments, both codon optimized and natural RdCVF and RdCVFL encoding sequences, in various combinations serve as the transgene.

A “vector” as used herein is a nucleic acid molecule into which an exogenous or heterologous or engineered nucleic acid transgene may be inserted which can then be introduced into an appropriate host cell. Vectors preferably have one or more origin of replication, and one or more site into which the recombinant DNA can be inserted. Vectors often have convenient means by which cells with vectors can be selected from those without, e.g., they encode drug resistance genes. Common vectors include plasmids, viral genomes, and (primarily in yeast and bacteria) “artificial chromosomes.” “Virus vectors” are defined as replication defective viruses containing the exogenous or heterologous RdCVF and RdCVFL nucleic acid transgene(s). In one embodiment a expression cassette as described herein may be engineered onto a plasmid which is used for drug delivery or for production of a viral vector. Suitable viral vectors are preferably replication defective and selected from amongst those which target ocular cells. Viral vectors may include any virus suitable for gene therapy may be used, including but not limited to adenovirus; herpes virus; lentivirus; retrovirus; parvovirus, etc. However, for ease of understanding, the adeno-associated virus is referenced herein as an exemplary virus vector.

A “replication-defective virus” or “viral vector” refers to a synthetic or recombinant viral particle in which an expression cassette containing a gene of interest is packaged in a viral capsid or envelope, where any viral genomic sequences also packaged within the viral capsid or envelope are replication-deficient; i.e., they cannot generate progeny virions but retain the ability to infect target cells. In one embodiment, the genome of the viral vector does not include genes encoding the enzymes required to replicate (the genome can be engineered to be “gutless”-containing only the transgene of interest flanked by the signals required for amplification and packaging of the artificial genome), but these genes may be supplied during production. Therefore, it is deemed safe for use in gene therapy since replication and infection by progeny virions cannot occur except in the presence of the viral enzyme required for replication.

In still another embodiment, the expression cassette, including any of those described herein is employed to generate a recombinant AAV genome.

As used herein, the term “host cell” may refer to the packaging cell line in which a recombinant AAV is produced from a proviral plasmid. In the alternative, the term “host cell” may refer to any target cell in which expression of the transgene is desired. Thus, a “host cell,” refers to a prokaryotic or eukaryotic cell that contains exogenous or heterologous DNA that has been introduced into the cell by any means, e.g., electroporation, calcium phosphate precipitation, microinjection, transformation, viral infection, transfection, liposome delivery, membrane fusion techniques, high velocity DNA-coated pellets, viral infection and protoplast fusion.

In certain embodiments herein, the term “host cell” refers to cultures of ocular cells of various mammalian species for in vitro assessment of the compositions described herein. In other embodiments herein, the term “host cell” refers to the cells employed to generate and package the viral vector or recombinant virus. Still in other embodiments, the term “host cell” is intended to reference the ocular cells of the subject being treated in vivo for the ocular disease.

As used herein, the term “ocular cells” refers to any cell in, or associated with the function of, the eye. The term may refer to any one of photoreceptor cells, including rod, cone and photosensitive ganglion cells or retinal pigment epithelium (RPE) cells. In one embodiment, the ocular cells are the photoreceptor cells.

“Plasmids” generally are designated herein by a lower case p preceded and/or followed by capital letters and/or numbers, in accordance with standard naming conventions that are familiar to those of skill in the art. Starting plasmids disclosed herein are either commercially available, publicly available on an unrestricted basis, or can be constructed from available plasmids by routine application of well known, published procedures. Many plasmids and other cloning and expression vectors that can be used in accordance with the present invention are well known and readily available to those of skill in the art. Moreover, those of skill readily may construct any number of other plasmids suitable for use in the invention. The properties, construction and use of such plasmids, as well as other vectors, in the present invention will be readily apparent to those of skill from the present disclosure.

As used herein, the term “transcriptional control sequence” or “expression control sequence” refers to DNA sequences, such as initiator sequences, enhancer sequences, and promoter sequences, which induce, repress, or otherwise control the transcription of protein encoding nucleic acid sequences to which they are operably linked.

As used herein, the term “operably linked” or “operatively associated” refers to both expression control sequences that are contiguous with the nucleic acid sequence encoding the RdCVF and RdCVFL and/or expression control sequences that act in trans or at a distance to control the transcription and expression thereof.

The term “AAV” or “AAV serotype” as used herein refers to the more than 30 naturally occurring and available adeno-associated viruses, as well as artificial AAVs. Among the AAVs isolated or engineered from human or non-human primates (NHP) and well characterized, human AAV2 is the first AAV that was developed as a gene transfer vector; it has been widely used for efficient gene transfer experiments in different target tissues and animal models. Unless otherwise specified, the AAV capsid, ITRs, and other selected AAV components described herein, may be readily selected from among any AAV, including, without limitation, AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV6.2, AAV7, AAV8, AAV9, rh10, AAVrh64R1, AAVrh64R2, rh8, rh.10, variants of any of the known or mentioned AAVs or AAVs yet to be discovered or variants or mixtures thereof. See, e.g., WO 2005/033321. The ITRs or other AAV components may be readily isolated or engineered using techniques available to those of skill in the art from an AAV. Such AAV may be isolated, engineered, or obtained from academic, commercial, or public sources (e.g., the American Type Culture Collection, Manassas, Va.). Alternatively, the AAV sequences may be engineered through synthetic or other suitable means by reference to published sequences such as are available in the literature or in databases such as, e.g., GenBank, PubMed, or the like. AAV viruses may be engineered by conventional molecular biology techniques, making it possible to optimize these particles for cell specific delivery of nucleic acid sequences, for minimizing immunogenicity, for tuning stability and particle lifetime, for efficient degradation, for accurate delivery to the nucleus, etc.

As used herein, “artificial AAV” means, without limitation, an AAV with a non-naturally occurring capsid protein. Such an artificial capsid may be generated by any suitable technique, using a selected AAV sequence (e.g., a fragment of a vp1 capsid protein) in combination with heterologous sequences which may be obtained from a different selected AAV, non-contiguous portions of the same AAV, from a non-AAV viral source, or from a non-viral source. An artificial AAV may be, without limitation, a pseudotyped AAV, a chimeric AAV capsid, a recombinant AAV capsid, or a “humanized” AAV capsid. Pseudotyped vectors, wherein the capsid of one AAV is replaced with a heterologous capsid protein, are useful in the invention. In one embodiment, AAV2/5 and AAV2/8 are exemplary pseudotyped vectors.

“Self-complementary AAV” refers a plasmid or vector having an expression cassette in which a coding region carried by a recombinant AAV nucleic acid sequence has been designed to form an intra-molecular double-stranded DNA template. Upon infection, rather than waiting for cell mediated synthesis of the second strand, the two complementary halves of scAAV will associate to form one double stranded DNA (dsDNA) unit that is ready for immediate replication and transcription. See, e.g., D M McCarty et al, “Self-complementary recombinant adeno-associated virus (scAAV) vectors promote efficient transduction independently of DNA synthesis”, Gene Therapy, (August 2001), Vol 8, Number 16, Pages 1248-1254. Self-complementary AAVs are described in, e.g., U.S. Pat. Nos. 6,596,535; 7,125,717; and 7,456,683, each of which is incorporated herein by reference in its entirety.

By “administering” as used in the methods means delivering the composition to the target selected cell which is characterized by the ocular disease. In one embodiment, the method involves delivering the composition by subretinal injection to the photoreceptor cells or other ocular cells. In another embodiment, intravitreal injection to ocular cells is employed. In still another method, injection via the palpebral vein to ocular cells may be employed. Still other methods of administration may be selected by one of skill in the art given this disclosure. By “administering” or “route of administration” is delivery of composition described herein, with or without a pharmaceutical carrier or excipient, of the subject. Routes of administration may be combined, if desired. In some embodiments, the administration is repeated periodically. The pharmaceutical compositions described herein are designed for delivery to subjects in need thereof by any suitable route or a combination of different routes. Direct delivery to the eye (optionally via ocular delivery, intra-retinal injection, intravitreal, topical), or delivery via systemic routes, e.g., intraarterial, intraocular, intravenous, intramuscular, subcutaneous, intradermal, and other parental routes of administration. The nucleic acid molecules and/or vectors described herein may be delivered in a single composition or multiple compositions. Optionally, two or more different AAV may be delivered, or multiple viruses [see, e.g., WO20 2011/126808 and WO 2013/049493]. In another embodiment, multiple viruses may contain different replication-defective viruses (e.g., AAV and adenovirus), alone or in combination with proteins.

The terms “a” or “an” refers to one or more, for example, “an inhibitor” is understood to represent one or more such compounds, molecules, peptides or antibodies. As such, the terms “a” (or “an”), “one or more,” and “at least one” are used interchangeably herein.

As used herein, the term “about” means a variability of plus or minus 10% from the reference given, unless otherwise specified.

The words “comprise”, “comprises”, and “comprising” are to be interpreted inclusively rather than exclusively, i.e., to include other unspecified components or process steps. The words “consist”, “consisting”, and its variants, are to be interpreted exclusively, rather than inclusively, i.e., to exclude components or steps not specifically recited.

Certain compositions described herein are isolated, or synthetically or recombinantly engineered nucleic acid sequences that provide novel codon-optimized sequences encoding hRdCVFL (long form) and hRdCVF (short form). In one embodiment, an isolated or engineered codon optimized nucleic acid sequence encoding human RdCVFL long form is provided. This codon-optimized RdCVFL SEQ ID NO: 1 contains an N-terminal SfiI and Kozak and C-terminal BglII restrictions sites added for cloning. When aligned with the native nucleic acid sequence, the codon optimized RdCVFL may have a percent identity of at least 50%, or at least 60%, or at least 70%, or at least 80% or at least 90%, including any integer between any of those ranges. In one embodiment, the codon optimized RdCVFL has a percent identify with the native sequence of at least 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99%. In one embodiment, when aligned with the native nucleic acid sequence SEQ ID NO: 3, it is revealed that codon optimized RdCVFL SEQ ID NO: 1 has a percent sequence identity of only 83% (see FIG. 3).

In another embodiment, an isolated codon optimized nucleic acid sequence encoding human RdCVF short form is provided. When aligned with the native nucleic acid sequence, the codon optimized RdCVF may have a percent identity of at least 50%, or at least 60%, or at least 70%, or at least 80% or at least 90%, including any integer between any of those ranges. In one embodiment, the codon optimized RdCVF has a percent identify with the native sequence of at least 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99%. In one embodiment, the codon-optimized RdCVF SEQ ID NO: 2 contains N-terminal NotI and Kozak and C-terminal BclI restrictions sites added for cloning. When aligned with the native nucleic acid sequence (nucleotides 1-327 of SEQ ID NO: 3), it is revealed that the encoding sequence of SEQ ID NO: 2 has a percent sequence identity of only 83% with the short form of the native sequence (see FIG. 4).

In one embodiment, the optimized nucleic acid sequences encoding the hRdCVF long and/or short constructs described herein are engineered into any suitable genetic element, e.g., naked DNA, phage, transposon, cosmid, RNA molecule (e.g., mRNA), episome, etc., which transfers the RdCVF sequences carried thereon to a host cell, e.g., for generating nanoparticles carrying DNA or RNA, viral vectors in a packaging host cell and/or for delivery to a host cells in subject. In one embodiment, the genetic element is a plasmid.

The selected genetic element may be delivered by any suitable method, including transfection, electroporation, liposome delivery, membrane fusion techniques, high velocity DNA-coated pellets, viral infection and protoplast fusion. The methods used to make such constructs are known to those with skill in nucleic acid manipulation and include genetic engineering, recombinant engineering, and synthetic techniques. See, e.g., Green and Sambrook, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, Cold Spring Harbor, N.Y. (2012).

A variety of expression cassettes are provided which employ SEQ ID NOs. 1 and 2 for expression of multiple or different versions of the hRdCVF protein. As used herein, an “expression cassette” refers to a nucleic acid molecule which comprises coding sequences for the optimized RdCVFL and/or RdCVF (short) proteins, promoter, and may include other regulatory sequences therefor, which cassette may be engineered into a genetic element or plasmid, and/or packaged into the capsid of a viral vector (e.g., a viral particle). In one embodiment, an expression cassette comprises a codon optimized nucleic acid sequence, i.e., SEQ ID NO: 1, that encodes RdCVFL. In one embodiment, the cassette provides the codon optimized RdCVFL operatively associated with expression control sequences that direct expression of the codon optimized nucleic acid sequence that encodes RdCVFL in a host cell.

In another embodiment, an expression cassette comprises a codon optimized nucleic acid sequence, i.e., SEQ ID NO: 2, that encodes RdCVF. In one embodiment, the cassette provides the codon optimized RdCVF operatively associated with expression control sequences that direct expression of the codon optimized nucleic acid sequence that encodes RdCVF in a host cell.

In still another embodiment, an expression cassette comprises a codon optimized nucleic acid sequence that encodes RdCVFL and RdCVF. In one embodiment of such an expression cassette, the sequence encoding RdCVFL is operatively associated with the a first expression control sequence(s) that direct expression of the codon optimized nucleic acid sequence that encodes RdCVFL in a host cell (a first transgene) and the sequence encoding RdCVF is operatively associated with the a second expression control sequence(s) that direct expression of the codon optimized nucleic acid sequence that encodes RdCVF in a host cell (a second transgene). Transcription of each optimized sequence is controlled by an independent expression control sequence and the transgenes are in tandem orientation within a single rAAV genome or expression cassette

In one embodiment, the second expression control sequence(s) are the copies of, but independent from, the first expression control sequence(s). In another embodiment, the second expression control sequence(s) are completely different and independent from, the first expression control sequence(s). In yet another embodiment, a single expression control sequence is operatively associated with both optimized sequences, so that both sequences are expressed at the same time under the same control sequences. In another embodiment, the two optimized sequences are expressed as a fusion sequence.

Further in one embodiment, the expression cassette comprises the hRdCVFL sequence under control of the first expression control sequence in position 5′ to the hRdCVF sequence, which is under control of the second expression control sequence. In another embodiment, the expression cassette comprises the hRdCVF sequence under control of the second expression control sequence in position 5′ to the hRdCVFL sequence, which is under control of the first expression control sequence. In yet another embodiment, where the expression cassette contains a single expression control sequence for control of transcription of both optimized sequences, the hRdCVF sequence is in position 5′ to the hRdCVFL sequence or the hRdCVFL sequence is in position 5′ to the hRdCVF sequence. In still other embodiments, the hRdCVF and hRdCVFL sequences may be in position to be expressed as a fusion protein.

In still another embodiment, an expression cassette comprises multiple copies of the RdCVF sequences, in which at one one copy is the codon optimized nucleic acid sequence, i.e., SEQ ID NO: 2, that encodes RdCVF. In one embodiment of such an expression cassette, the sequence encoding codon optimized RdCVF is operatively associated with the a first expression control sequence(s) that direct expression of the codon optimized nucleic acid sequence that encodes one copy of RdCVF in a host cell and the sequence encoding the second copy of codon-optimized RdCVF is operatively associated with a second expression control sequence(s) that direct expression of the codon optimized nucleic acid sequence that encodes the second copy of RdCVF in a host cell, i.e., transcription of each optimized sequence is controlled by an independent expression control sequence. In one embodiment, the second expression control sequence(s) are the copies of, but independent from, the first expression control sequence(s). In another embodiment, the second expression control sequence(s) are completely different and independent from, the first expression control sequence(s).

Similarly, in still another embodiment, an expression cassette comprises multiple copies of the RdCVFL sequences, in which at one one copy is the codon optimized nucleic acid sequence, i.e., SEQ ID NO: 1, that encodes RdCVFL. In one embodiment of such an expression cassette, the sequence encoding codon optimized RdCVFL is operatively associated with the a first expression control sequence(s) that direct expression of the codon optimized nucleic acid sequence that encodes one copy of RdCVFL in a host cell and the sequence encoding the second copy of codon-optimized RdCVFL is operatively associated with a second expression control sequence(s) that direct expression of the codon optimized nucleic acid sequence that encodes the second copy of RdCVFL in a host cell, i.e., transcription of each optimized sequence is controlled by an independent expression control sequence. In one embodiment, the second expression control sequence(s) are the copies of, but independent from, the first expression control sequence(s). In another embodiment, the second expression control sequence(s) are completely different and independent from, the first expression control sequence(s).

In yet another embodiment, a single expression control sequence is operatively associated with both optimized sequences, so that both sequences are expressed at the same time under the same control sequences. In another embodiment, the two optimized sequences are expressed as a fusion sequence. In still other embodiments, the optimized RdCVF is present in the expression cassette with a native version of the RdCVF sequence.

As described above for the expression cassettes containing both RdCVF and RdCVFL, in embodiments in which two different versions of RdCVF are employed, the codon optimized sequence may be positioned, 5′ or 3′ to another version of the short sequences. One of skill in the art may readily design constructs similar to those of the Examples below in view of the teachings of this specification.

As described herein, a “rAAV genome” is meant to describe an expression cassette or an expression cassette containing tandem transgenes, as described herein flanked on its 5′ end by a 5′AAV inverted terminal repeat sequence (ITR) and on its 3′ end by a 3′ AAV ITR. Thus, this rAAV genome contains the minimal sequences required to package the expression cassette into an AAV viral particle, i.e., the AAV 5′ and 3′ ITRs. The AAV ITRs may be obtained from the ITR sequences of any AAV, such as described herein. These ITRs may be of the same AAV origin as the capsid employed in the resulting recombinant AAV, or of a different AAV origin (to produce an AAV pseudotype). In one embodiment, the ITR sequences from AAV2, or the deleted version thereof (ΔITR), are used for convenience and to accelerate regulatory approval. However, ITRs from other AAV sources may be selected. Each rAAV genome can be then introduced into a proviral plasmid following the teachings of WO2012/158757. The proviral plasmids are cultured in the host cells which express the AAV cap and/or rep proteins. In the host cells, each rAAV genome is rescued and packaged into the capsid protein or envelope protein to form an infectious viral particle.

In yet another embodiment, a vector comprising any of the expression cassettes described herein is provided. As described above, such vectors can be plasmids of variety of origins and are useful in certain embodiments for the generation of recombinant replication defective viruses as described further herein.

In one another embodiment, the vector is a proviral plasmid that comprises an AAV capsid and an recombinant AAV genome, wherein said rAAV genome comprises AAV inverted terminal repeat sequences and an expression cassette as described above comprising a codon optimized nucleic acid sequence that encodes RdCVFL, RdCVF, both RdCVFL and RdCVF or multiple (i.e., at least two) copies of RdCVF or two copies of RdCVFL, and expression control sequences that direct expression of the encoded protein in a host cell.

One type of proviral plasmid comprises a modular recombinant AAV genome that permits portions of the components of the rAAV genome to be removed and repeatedly replaced with other components without destroying the restriction sites in the plasmid. Such a proviral plasmid is one that contains a 5′ AAV ITR sequence, the ITR flanked upstream by restriction site 1 and downstream by restriction site 2; a selected promoter flanked upstream by restriction site 2 and downstream by restriction site 3. Another component of the modular rAAV is a polylinker sequence comprising at least restriction site 3, restriction site 4 and restriction site 5, that contains a codon optimized nucleic acid sequence that encodes RdCVFL, a codon optimized nucleic acid sequence that encodes RdCVF, a codon optimized nucleic acid sequence that encodes RdCVFL and a codon optimized nucleic acid sequence that encodes RdCVF, or two or more copies of a sequence that encodes RdCVF, at least one such sequence being a codon optimized nucleic acid sequence encoding RdCVF. The RdCVF encoding sequences are located between any two of the restriction sites 3, 4 and 5, and are operatively linked to, and under the regulatory control of, the promoter. Alternatively, the second encoding sequence is inserted into the polylinker sequence along with the second expression control sequence of the expression cassette as described above.

Additional components of the modular rAAV include a polyadenylation sequence flanked upstream by restriction site 4 or 5 and downstream by restriction site 6; and a 3′ AAV ITR sequence flanked upstream by restriction site 6 and downstream by restriction site 7. The proviral plasmid also contains elements necessary for replication in bacterial cells, and a resistance gene. Each of the above-noted restriction sites 1 through 7 occurs only once in the proviral plasmid and is cleaved by a different enzyme that cannot cleave another restriction site in the plasmid and thereby permit independent and repeated removal, replacement or substitution of the entire rAAV modular genome or only the elements flanked by those restriction sites from the plasmid. Such plasmids are described in detail in International Patent Application Publication No. WO2012/158757, incorporated by reference herein.

In still a further embodiment, a recombinant adeno-associated virus (AAV) vector is provided for delivery of the RdCVF constructs and optimized sequences described herein. An adeno-associated virus (AAV) viral vector is an AAV DNase-resistant particle having an AAV protein capsid into which is packaged nucleic acid sequences for delivery to target cells. An AAV capsid is composed of 60 capsid (cap) protein subunits, VP1, VP2, and VP3, that are arranged in an icosahedral symmetry in a ratio of approximately 1:1:10 to 1:1:20, depending upon the selected AAV. AAVs may be selected as sources for capsids of AAV viral vectors as identified above. See, e.g., US Published Patent Application No. 2007-0036760-A1; US Published Patent Application No. 2009-0197338-A1; EP 1310571. See also, WO 2003/042397 (AAV7 and other simian AAV), U.S. Pat. Nos. 7,790,449 and 7,282,199 (AAV8), WO 2005/033321 and U.S. Pat. No. 7,906,111 (AAV9), and WO 2006/110689, and WO 2003/042397 (rh.10). These documents also describe other AAV which may be selected for generating AAV and are incorporated by reference. In some embodiments, an AAV cap for use in the viral vector can be generated by mutagenesis (i.e., by insertions, deletions, or substitutions) of one of the aforementioned AAV capsids or its encoding nucleic acid. In some embodiments, the AAV capsid is chimeric, comprising domains from two or three or four or more of the aforementioned AAV capsid proteins. In some embodiments, the AAV capsid is a mosaic of Vp1, Vp2, and Vp3 monomers from two or three different AAVs or recombinant AAVs. In some embodiments, an rAAV composition comprises more than one of the aforementioned Caps.

In another embodiment, the AAV capsid includes variants which may include up to about 10% variation from any described or known AAV capsid sequence. That is, the AAV capsid shares about 90% identity to about 99.9% identity, about 95% to about 99% identity or about 97% to about 98% identity to an AAV capsid provided herein and/or known in the art. In one embodiment, the AAV capsid shares at least 95% identity with an AAV capsid. When determining the percent identity of an AAV capsid, the comparison may be made over any of the variable proteins (e.g., vp1, vp2, or vp3). In one embodiment, the AAV capsid shares at least 95% identity with the AAV8 vp3. In another embodiment, a self-complementary AAV is used.

For packaging an expression cassette or rAAV genome or proviral plasmid into virions, the ITRs are the only AAV components required in cis in the same construct as the transgene. In one embodiment, the coding sequences for the replication (rep) and/or capsid (cap) are removed from the AAV genome and supplied in trans or by a packaging cell line in order to generate the AAV vector. For example, as described above, a pseudotyped AAV may contain ITRs from a source which differs from the source of the AAV capsid. Additionally or alternatively, a chimeric AAV capsid may be utilized. Still other AAV components may be selected. Sources of such AAV sequences are described herein and may also be isolated or engineered obtained from academic, commercial, or public sources (e.g., the American Type Culture Collection, Manassas, Va.). Alternatively, the AAV sequences may be obtained through synthetic or other suitable means by reference to published sequences such as are available in the literature or in databases such as, e.g., GenBank®, PubMed®, or the like.

Methods for generating and isolating AAV viral vectors suitable for delivery to a subject are known in the art. See, e.g., U.S. Pat. Nos. 7,790,449; 7,282,199; WO 2003/042397; WO 2005/033321, WO 2006/110689; and U.S. Pat. No. 7,588,772 B2. In a one system, a producer cell line is transiently transfected with a construct that encodes the transgene flanked by ITRs and a construct(s) that encodes rep and cap. In a second system, a packaging cell line that stably supplies rep and cap is transiently transfected with a construct encoding the transgene flanked by ITRs. In each of these systems, AAV virions are produced in response to infection with helper adenovirus or herpesvirus, requiring the separation of the rAAVs from contaminating virus. More recently, systems have been developed that do not require infection with helper virus to recover the AAV—the required helper functions (i.e., adenovirus E1, E2a, VA, and E4 or herpesvirus UL5, UL8, UL52, and UL29, and herpesvirus polymerase) are also supplied, in trans, by the system. In these newer systems, the helper functions can be supplied by transient transfection of the cells with constructs that encode the required helper functions, or the cells can be engineered to stably contain genes encoding the helper functions, the expression of which can be controlled at the transcriptional or posttranscriptional level.

In yet another system, the transgene flanked by ITRs and rep/cap genes are introduced into insect cells by infection with baculovirus-based vectors. For reviews on these production systems, see generally, e.g., Zhang et al., 2009, “Adenovirus-adeno-associated virus hybrid for large-scale recombinant adeno-associated virus production,” Human Gene Therapy 20:922-929, the contents of each of which is incorporated herein by reference in its entirety. Methods of making and using these and other AAV production systems are also described in the following U.S. patents, the contents of each of which is incorporated herein by reference in its entirety: U.S. Pat. Nos. 5,139,941; 5,741,683; 6,057,152; 6,204,059; 6,268,213; 6,491,907; 6,660,514; 6,951,753; 7,094,604; 7,172,893; 7,201,898; 7,229,823; and 7,439,065. See generally, e.g., Grieger & Samulski, 2005, “Adeno-associated virus as a gene therapy vector: Vector development, production and clinical applications,” Adv. Biochem. Engin/Biotechnol. 99: 119-145; Buning et al., 2008, “Recent developments in adeno-associated virus vector technology,” J. Gene Med. 10:717-733; and the references cited below, each of which is incorporated herein by reference in its entirety.

The methods used to construct any embodiment of this invention are known to those with skill in nucleic acid manipulation and include genetic engineering, recombinant engineering, and synthetic techniques. See, e.g., Green and Sambrook et al, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, Cold Spring Harbor, N.Y. (2012). Similarly, methods of generating rAAV virions are well known and the selection of a suitable method is not a limitation on the present invention. See, e.g., K. Fisher et al, (1993) J. Virol., 70:520-532 and U.S. Pat. No. 5,478,745.

The rAAV vectors comprise an AAV capsid and an recombinant AAV genome, such as described above. In certain embodiments, the rAAV genome comprises AAV inverted terminal repeat sequences and an expression cassette comprising a codon optimized nucleic acid sequence that encodes RdCVFL, RdCVF, both RdCVFL and RdCVF or at least two copies of RdCVF, or two copies of RdCVFL, with at least one copy optimized or two copies optimized, and expression control sequences that direct expression of the encoded proteins in a host cell. The rAAV, in other embodiments, further comprises one or more of an intron, a Kozak sequence, a poly A, and post-transcriptional regulatory elements. Such rAAV vectors for use in pharmaceutical compositions for delivery to the eye, may employ a capsid from any of the many known AAVs identified above.

Other conventional components of the expression cassettes, rAAV genomes, and vectors include other components that can be optimized for a specific species using techniques known in the art including, e.g., codon optimization, as described herein. The components of the cassettes, vectors, plasmids and viruses or other compositions described herein include a promoter sequence as part of the expression control sequences. In one embodiment, a suitable promoter is a hybrid chicken (β-actin (CBA)promoter with cytomegalovirus (CMV) enhancer elements, such as the promoter used in the examples below and represented by the nucleic acid sequences of Tables 1 and 2A and 2B, i.e., nucleotides 307-1578 of SEQ ID NO: 5. Still other suitable promoters are the CB7 promoter, as well such as viral promoters, constitutive promoters, regulatable promoters [see, e.g., WO 2011/126808 and WO 2013/04943], or a promoter responsive to physiologic cues may be used may be utilized in the expression cassette, rAAV genomes, vectors, plasmids and viruses described herein.

In another embodiment, the promoter is cell-specific. The term “cell-specific” means that the particular promoter selected for the recombinant vector can direct expression of the optimized RdCVF transgene in a particular ocular cell type. In one embodiment, the promoter is specific for expression of the transgene in photoreceptor cells. In another embodiment, the promoter is specific for expression in the rods and cones. In another embodiment, the promoter is specific for expression in the rods. In another embodiment, the promoter is specific for expression in the cones.

Exemplary promoters may be the human G-protein-coupled receptor protein kinase 1 (GRK1) promoter (Genbank Accession number AY327580). In another embodiment, the promoter is a 292 nt fragment (positions 1793-2087) of the GRK1 promoter (See, Beltran et al, Gene Therapy 2010 17:1162-74, which is hereby incorporated by reference herein). In another preferred embodiment, the promoter is the human interphotoreceptor retinoid-binding protein proximal (IRBP) promoter. In one embodiment, the promoter is a 235 nt fragment of the hIRBP promoter. In one embodiment, the promoter is the RPGR proximal promoter (Shu et al, IOVS, May 2102, which is incorporated by reference herein). Other promoters useful in the invention include, without limitation, the rod opsin promoter, the red-green opsin promoter, the blue opsin promoter, the cGMP-β-phosphodiesterase promoter, the mouse opsin promoter (Beltran et al 2010 cited above), the rhodopsin promoter (Mussolino et al, Gene Ther, July 2011, 18(7):637-45); the alpha-subunit of cone transducin (Morrissey et al, BMC Dev, Biol, January 2011, 11:3); beta phosphodiesterase (PDE) promoter; the retinitis pigmentosa (RP1) promoter (Nicord et al, J. Gene Med, December 2007, 9(12):1015-23); the NXNL2/NXNL1 promoter (Lambard et al, PLoS One, October 2010, 5(10):e13025), the RPE65 promoter; the retinal degeneration slow/peripherin 2 (Rds/perph2) promoter (Cai et al, Exp Eye Res. 2010 August; 91(2):186-94); and the VMD2 promoter (Kachi et al, Human Gene Therapy, 2009 (20:31-9)). Each of these documents is incorporated by reference herein. In one embodiment, the promoter is of a small size, under 1000 bp, due to the size limitations of the AAV vector. In another embodiment, the promoter is under 400 bp. Other promoters may be selected by one of skill in the art.

In other embodiments, the cassette, vector, plasmid and virus constructs described herein contain other appropriate transcription initiation, termination, enhancer sequences, efficient RNA processing signals such as splicing and polyadenylation (poly A) signals; TATA sequences; sequences that stabilize cytoplasmic mRNA; sequences that enhance translation efficiency (i.e., Kozak consensus sequence); introns; sequences that enhance protein stability; and when desired, sequences that enhance secretion of the encoded product. The expression cassette or vector may contain none, one or more of any of the elements described herein. Examples of suitable poly A sequences include, e.g., SV40, bovine growth hormone (bGH), and TK poly A. Examples of suitable enhancers include, e.g., the CMV enhancer, the RSV enhancer, the alpha fetoprotein enhancer, the TTR minimal promoter/enhancer, LSP (TH-binding globulin promoter/alpha1-microglobulin/bikunin enhancer), amongst others.

In yet other aspects, these nucleic acid sequences, vectors, rAAV genomes and rAAV viral vectors are useful in a pharmaceutical composition, which also comprises a pharmaceutically acceptable carrier. Such pharmaceutical compositions are used to express the optimized RdCVFL or RdCVF, or multiple copies of RdCVF or both proteins in the ocular cells through delivery by such recombinantly engineered AAVs or artificial AAV's.

To prepare these pharmaceutical compositions containing the nucleic acid sequences, vectors, rAAV genomes and rAAV viral vectors, the sequences or vectors or viral vector is preferably assessed for contamination by conventional methods and then formulated into a pharmaceutical composition suitable for administration to the eye. Such formulation involves the use of a pharmaceutically and/or physiologically acceptable vehicle or carrier, particularly one suitable for administration to the eye, such as buffered saline or other buffers, e.g., HEPES, to maintain pH at appropriate physiological levels, and, optionally, other medicinal agents, pharmaceutical agents, stabilizing agents, buffers, carriers, adjuvants, diluents, etc. For injection, the carrier will typically be a liquid. Exemplary physiologically acceptable carriers include sterile, pyrogen-free water and sterile, pyrogen-free, phosphate buffered saline. A variety of such known carriers are provided in U.S. Pat. No. 7,629,322, incorporated herein by reference. In one embodiment, the carrier is an isotonic sodium chloride solution. In another embodiment, the carrier is balanced salt solution. In one embodiment, the carrier includes tween. If the virus is to be stored long-term, it may be frozen in the presence of glycerol or Tween20.

In one exemplary specific embodiment, the composition of the carrier or excipient contains 180 mM NaCl, 10 mM NaPi, pH 7.3 with 0.0001%-0.01% Pluronic F68 (PF68). The exact composition of the saline component of the buffer ranges from 160 mM to 180 mM NaCl. Optional a different pH buffer (potentially HEPEs, sodium bicarbonate, TRIS) is used in place of the buffer specifically described. Still alternatively, a buffer containing 0.9% NaCl is useful.

Optionally, the compositions of the invention may contain, in addition to the rAAV and/or variants and carrier(s), other conventional pharmaceutical ingredients, such as preservatives, or chemical stabilizers. Suitable exemplary preservatives include chlorobutanol, potassium sorbate, sorbic acid, sulfur dioxide, propyl gallate, the parabens, ethyl vanillin, glycerin, phenol, and parachlorophenol. Suitable chemical stabilizers include gelatin and albumin.

The pharmaceutical compositions containing the replication-defective rAAV viruses can be formulated with a physiologically acceptable carrier for use in gene transfer and gene therapy applications. In the case of AAV viral vectors, quantification of the genome copies (“GC”), vector genomes, or virus particles may be used as the measure of the dose contained in the formulation or suspension. Any method known in the art can be used to determine the genome copy (GC) number of the replication-defective virus compositions of the invention. One method for performing AAV GC number titration is as follows: Purified AAV vector samples are first treated with DNase to eliminate un-encapsidated AAV genome DNA or contaminating plasmid DNA from the production process. The DNase resistant particles are then subjected to heat treatment to release the genome from the capsid. The released genomes are then quantitated by real-time PCR using primer/probe sets targeting specific region of the viral genome (usually poly A signal). In another method the effective dose of a recombinant adeno-associated virus carrying a nucleic acid sequence encoding the optimized RdCVF transgene under the desirably are measured as described in S. K. McLaughlin et al, 1988 J. Virol., 62:1963.

As used herein, the term “dosage” can refer to the total dosage delivered to the subject in the course of treatment, or the amount delivered in a single unit (or multiple unit or split dosage) administration. The pharmaceutical virus compositions can be formulated in dosage units to contain an amount of replication-defective virus carrying the codon optimized nucleic acid sequences encoding hRdCVF and/or hRdCVFL as described herein that is in the range of about 1.0×10⁹ GC to about 1.0×10¹⁵ GC including all integers or fractional amounts within the range. In one embodiment, the compositions are formulated to contain at least 1×10⁹, 2×10⁹, 3×10⁹, 4×10⁹, 5×10⁹, 6×10⁹, 7×10⁹, 8×10⁹, or 9×10⁹ GC per dose including all integers or fractional amounts within the range. In another embodiment, the compositions are formulated to contain at least 1×10¹⁰, 2×10¹⁰, 3×10¹⁰, 4×10¹⁰, 5×10¹⁰, 6×10¹⁰, 7×10¹⁰, 8×10¹⁰, or 9×10¹⁰ GC per dose including all integers or fractional amounts within the range. In another embodiment, the compositions are formulated to contain at least 1×10¹¹, 2×10¹¹, 3×10¹¹, 4×10¹¹, 5×10¹¹, 6×10¹¹, 7×10¹¹, 8×10¹¹, or 9×10¹¹ GC per dose including all integers or fractional amounts within the range. In another embodiment, the compositions are formulated to contain at least 1×10¹², 2×10¹², 3×10¹², 4×10¹², 5×10¹², 6×10¹², 7×10¹², 8×10¹², or 9×10¹² GC per dose including all integers or fractional amounts within the range. In another embodiment, the compositions are formulated to contain at least 1×10¹³, 2×10¹³, 3×10¹³, 4×10¹³, 5×10¹³, 6×10¹³, 7×10¹³, 8×10¹³, or 9×10¹³ GC per dose including all integers or fractional amounts within the range. In another embodiment, the compositions are formulated to contain at least 1×10¹⁴, 2×10¹⁴, 3×10¹⁴, 4×10¹⁴, 5×10¹⁴, 6×10¹⁴, 7×10¹⁴, 8×10¹⁴, or 9×10¹⁴ GC per dose including all integers or fractional amounts within the range. In another embodiment, the compositions are formulated to contain at least 1×10¹⁵, 2×10¹⁵, 3×10¹⁵, 4×10¹⁵, 5×10¹⁵, 6×10¹⁵, 7×10¹⁵, 8×10¹⁵, or 9×10¹⁵ GC per dose including all integers or fractional amounts within the range. In one embodiment, for human application the dose can range from 1×10¹⁰ to about 1×10¹² GC per dose including all integers or fractional amounts within the range.

These above doses may be administered in a variety of volumes of carrier, excipient or buffer formulation, ranging from about 25 to about 1000 microliters, including all numbers within the range, depending on the size of the area to be treated, the viral titer used, the route of administration, and the desired effect of the method. In one embodiment, the volume of carrier, excipient or buffer is at least about 25 μl. In one embodiment, the volume is about 50 μl. In another embodiment, the volume is about 75 μl. In another embodiment, the volume is about 100 μl. In another embodiment, the volume is about 125 μl. In another embodiment, the volume is about 150 μl. In another embodiment, the volume is about 175 μl. In yet another embodiment, the volume is about 200 μL. In another embodiment, the volume is about 225 μl. In yet another embodiment, the volume is about 250 μl. In yet another embodiment, the volume is about 275 μl. In yet another embodiment, the volume is about 300 μL. In yet another embodiment, the volume is about 325 μL. In another embodiment, the volume is about 350 μl. In another embodiment, the volume is about 375 μl. In another embodiment, the volume is about 400 μl. In another embodiment, the volume is about 450 μl. In another embodiment, the volume is about 500 μl. In another embodiment, the volume is about 550 μl. In another embodiment, the volume is about 600 μl. In another embodiment, the volume is about 650 μl. In another embodiment, the volume is about 700 μl. In another embodiment, the volume is between about 700 and 1000 μl.

In one embodiment, the viral constructs may be delivered in concentrations of from at least least 1×10⁹ to about least 1×10¹¹ GCs in volumes of about 1 μl to about 3 μl for small animal subjects, such as mice. For larger veterinary subjects having eyes about the same size as human eyes, the larger human dosages and volumes stated above are useful. See, e.g., Diehl et al, J. Applied Toxicology, 21:15-23 (2001) for a discussion of good practices for administration of substances to various veterinary animals. This document is incorporated herein by reference.

It is desirable that the lowest effective concentration of virus or other delivery vehicle be utilized in order to reduce the risk of undesirable effects, such as toxicity, retinal dysplasia and detachment. Still other dosages in these ranges may be selected by the attending physician, taking into account the physical state of the subject, preferably human, being treated, the age of the subject, the particular ocular disorder and the degree to which the disorder, if progressive, has developed.

Yet another aspect described herein is a method for treating, retarding or halting progression of blindness in a mammalian subject having one or more of the ocular diseases described above, such as rod-cone dystrophies or retinal degenerative disease. The rAAV, preferably suspended in a physiologically compatible carrier, diluent, excipient and/or adjuvant, may be administered to a desired subject including without limitation, a cat, dog, or other non-human mammalian subject. This method comprises administering to a subject in need thereof any of the nucleic acid sequences, expression cassettes, rAAV genomes, plasmids, vectors or rAAV vectors or compositions containing them. In one embodiment, the composition is delivered subretinally. In another embodiment, the composition is delivered intravitreally. In still another embodiment, the composition is delivered using a combination of administrative routes suitable for treatment of ocular diseases, and may also involve administration via the palpebral vein or other intravenous or conventional administration routes.

For use in these methods, the volume and viral titer of each dosage is determined individually, as further described herein, and may be the same or different from other treatments performed in the same, or contralateral, eye. In another embodiment, a single, larger volume treatment is made in order to treat the entire eye. The dosages, administrations and regimens may be determined by the attending physician given the teachings of this specification.

In one embodiment, the composition is administered in a single dosage selected from those above listed in a single affected eye. In another embodiment, the composition is administered as a single dosage selected from those above listed in a both affected eyes, either simultaneously or sequentially. Sequential administration may imply a time gap of administration from one eye to another from intervals of minutes, hours, days, weeks or months. In another embodiment, the method involves administering the compositions to an eye two or more dosages (e.g., split dosages).

In still other embodiments, the compositions described herein may be delivered in a single composition or multiple compositions. Optionally, two or more different AAV may be delivered, or multiple viruses [see, e.g., WO 2011/126808 and WO 2013/049493]. In another embodiment, multiple viruses may contain different replication-defective viruses (e.g., AAV and adenovirus).

In certain embodiments of the invention it is desirable to perform non-invasive retinal imaging and functional studies to identify areas of the rod and cone photoreceptors to be targeted for therapy. In these embodiments, clinical diagnostic tests are employed to determine the precise location(s) for one or more subretinal injection(s). These tests may include electroretinography (ERG), perimetry, topographical mapping of the layers of the retina and measurement of the thickness of its layers by means of confocal scanning laser ophthalmoscopy (cSLO) and optical coherence tomography (OCT), topographical mapping of cone density via adaptive optics (AO), functional eye exam, etc, depending upon the species of the subject being treated, their physical status and health and the dosage. In view of the imaging and functional studies, in some embodiments of the invention one or more injections are performed in the same eye in order to target different areas of the affected eye. The volume and viral titer of each injection is determined individually, as further described below, and may be the same or different from other injections performed in the same, or contralateral, eye. In another embodiment, a single, larger volume injection is made in order to treat the entire eye. In one embodiment, the volume and concentration of the rAAV composition is selected so that only the region of damaged rod and cone receptors is impacted. In another embodiment, the volume and/or concentration of the rAAV composition is a greater amount, in order reach larger portions of the eye, including non-damaged photoreceptors.

In one embodiment of the methods described herein, a one-time intra-ocular delivery of a composition such as those described herein, e.g., an AAV delivery of an optimized RdCVF or RdCVFL cassette, is useful in preventing vision loss and blindness in millions of individuals affected with such ocular disorders or multi-systemic diseases without regard to genotype or environmental exposure.

Thus, in one embodiment, the composition is administered before disease onset. In another embodiment, the composition is administered prior to the initiation of vision impairment or loss. In another embodiment, the composition is administered after initiation of vision impairment or loss. In yet another embodiment, the composition is administered when less than 90% of the rod and/or cones or photoreceptors are functioning or remaining, as compared to a non-diseased eye.

In another embodiment, the method includes performing additional studies, e.g., functional and imaging studies to determine the efficacy of the treatment. For examination in animals, such tests include retinal and visual function assessment via electroretinograms (ERGs) looking at rod and cone photoreceptor function, optokinetic nystagmus, pupillometry, water maze testing, light-dark preference histology (retinal thickness, rows of nuclei in the outer nuclear layer, immunofluorescence to document transgene expression, cone photoreceptor counting, staining of retinal sections with peanut agglutinin—which identifies cone photoreceptor sheaths). Other suitable tests of efficacy are sampling of anterior chamber fluid to document presence of the RdCVF and RdCVFL transgenic proteins.

Specifically for human subjects, following administration of a dosage of a compositions described in this specification, the subject is tested for efficacy of treatment using electroretinograms (ERGs) to examine rod and cone photoreceptor function, pupillometry visual acuity, contrast sensitivity color vision testing, visual field testing (Humphrey visual fields/Goldmann visual fields), perimetry mobility test (obstacle course), and reading speed test. Other useful post-treatment efficacy test to which the subject is exposed following treatment with a pharmaceutical composition described herein are functional magnetic resonance imaging (fMRD, full-field light sensitivity testing, retinal structure studies including optical coherence tomography, fundus photography, fundus autofluorescence, adaptive optics scanning, and/or laser ophthalmoscopy. These and other efficacy tests are described in U.S. Pat. No. 8,147,823; in co-pending International patent application publication WO 2014/011210 or WO 2014/124282, incorporated by reference.

In yet another embodiment, any of the above described methods is performed in combination with another, or secondary, therapy. In still other embodiments, the methods of treatment of these ocular diseases involve treating the subject with the composition described in detail herein in combination with another therapy, such as antibiotic treatment, palliative treatment for pain, and the like. The additional therapy may be any now known, or as yet unknown, therapy which helps prevent, arrest or ameliorate these mutations or defects or any of the effects associated therewith. The secondary therapy can be administered before, concurrent with, or after administration of the compositions described above. In one embodiment, a secondary therapy involves non-specific approaches for maintaining the health of the retinal cells, such as administration of neurotrophic factors, anti-oxidants, anti-apoptotic agents. The non-specific approaches are achieved through injection of proteins, recombinant DNA, recombinant viral vectors, stem cells, fetal tissue, or genetically modified cells. The latter could include genetically modified cells that are encapsulated.

In one embodiment, a method of generating a recombinant rAAV comprises obtaining a plasmid containing a rAAV genome as described above and culturing a packaging cell carrying the plasmid in the presence of sufficient viral sequences to permit packaging of the AAV viral genome into an infectious AAV envelope or capsid. Specific methods of rAAV vector generation are described above and may be employed in generating a rAAV vector that can deliver one or more of the codon optimized RdCVFL or RdCVF in the expression cassettes and genomes described above and in the examples below.

The following examples disclose specific embodiments of the nucleic acid sequences, expression cassettes, rAAV genome and viral vectors for use in treating the ocular diseases specified herein. These specific embodiments illustrate various aspects of the invention. These examples should be construed to encompass any and all variations that become evident as a result of the teaching provided herein.

Example 1 Codon Optimized Sequences

The nucleic acid sequence SEQ ID NO: 1 (FIG. 1) encoding codon optimized human RdCVFL was generated to add N-terminal restriction site SfiI and C terminal restriction site BglII, as well as Kozak sequences. The open reading frame (ORF) of codon optimized SEQ ID NO:1 differs from the native sequence by 17%, i.e., it shares only 83% identity with native hRdCVF, as shown in FIG. 3.

The nucleic acid sequence SEQ ID NO: 2 (FIG. 1) encoding codon optimized human RdCVF was generated to add N-terminal restriction site NotI and C terminal restriction site BclII, as well as Kozak sequences. The ORF of codon optimized SEQ ID NO:2 differs from the native sequence by 17%, sharing only 83% identity with native hRdCVF, as shown in FIG. 4.

Example 2 Construction of P853

SEQ ID NO: 2 was cloned into an expression vector under the control of a chicken-beta actin promoter with CMV enhancer, the promoter truncated by 390 nucleotides. SEQ ID NO: 1 was cloned into the same cassette under the control of a second copy of the same promoter. The expression construct was flanked by AAV2 ITRs thus forming the p853 rAAV genome p853 (See FIG. 5). This rAAV genome was then inserted into a proviral plasmid, p618 containing a lambda stuffer sequence (see International Patent Application Publication No. WO2012/158757A1), thereby generating the proviral plasmid p853 which permits expression of both the long and short RdCVF proteins in a single vector.

The features of the rAAV genome of FIG. 5 SEQ ID NO: 4 and the p853 plasmid pAAV.CMV.CBA.hRdCVF.CMV.CBA.hRDCVFL.SYNITR.Long SEQ ID NO: 7 containing the rAAV genome of FIG. 5 and other plasmid sequences are described below in Table 1, with reference to the nucleotide positions (Nts) in each sequence.

TABLE 1 SEQUENCES rAAV Genome Cassette Nts of SEQ ID pAAV.CMV.CBA.hRdCVF.CMV.CBA.hRdCVFL.SYNITR.long Sequence Feature NO: 4 Nts of SEQ ID NO: 7 Kan^(R) Complement —  9-803 B1 B2 T1 Txn —  988-1162 Terminator Complement pTR — 1063-1079 5′ ITR (D Segment)  17-146 1253-1382 (129-146) (1365-1382) Promoter Delta 390  207-1478 1443-2714 hRdCVF 1479-1826 2715-3062 Poly A 1821-2047 3057-3283 Terminator 2042-2479 3278 -3715  (Promoter) With (2490-3761) (3726-4997) Flanking Restriction 2474-3774 3710-5010 Sites hRDCVFL 3762-4426 4998-5662 (Bgl) Poly A 4427-4643 5663-5879 3′ ITR (D Segment) 4691-4820 5927-6056 (4691-4708) (5927-5944) pTF3 Complement — 6241-6266 BLA Txn Terminator — 6150-6450 RPN Txn Terminator — 6457-6570 Lambda Stuffer —  6586-11652 pUC Ori Complement — 11813-12616

Example 3 Construction of rAAV Co-Expressing hRdCVF and hRdCVFL

The rAAV genome from this p853 proviral plasmid SEQ ID NO: 7 is packaged in a selected AAV capsid by culturing a packaging cell carrying the plasmid in the presence of sufficient viral sequences to permit packaging of the AAV genome into an infectious AAV envelope or capsid. In one embodiment, a method for producing the rAAV involves packaging in a stable rep and cap expressing mammalian host packaging cell line (such as B-50 as described in International Patent Application Publication No. WO 99/15685) with the adenovirus E1, E2a, and E4ORF6 DNA. Iodixanol gradient purification is followed by herparin-sepharose agarose column chromatography. Vector titers are determined using an infectious center assay.

Recombinant AAV.CMV.CBA.hRdCVF.CMV.CBA.hRdCVFL. SYNITR.Long virus preparations are prepared in and combined to a desired total volume.

Still other methods of producing such rAAV particles involve use of an insect cell packaging cell line, such as described in Smith et al, ref 11, cited below.

The AAV.CMV.CBA.hRdCVF.CMV.CBA.hRdCVFL.SYNITR.Long viral particles are suspended in a suitable excipient, such as 180 mM NaCl, 10 mM NaPi, pH7.3, containing 0.0001%-0.01% Pluronic F68 (PF68). The composition of the saline component ranges from 160 mM to 180 mM NaCl. Other buffers are useful in such compositions, including HEPEs, sodium bicarbonate, TRIS, or 0.9% NaCl solution.

Several preparations of the rAAV are combined to a desired total volume. In one embodiment, a total volume is a dosage of 1×0¹¹ GC in a volume of 300 microliters of buffer. Contaminating helper adenovirus and native AAV, assayed by serial dilution cytopathic effect or infectious center assay, respectively are anticipated to be less than one or multiples orders of magnitude lower than vector AAV.

Example 4 Construction of rAAV Expressing 2XRdCVF

A native short form of RdCVF (or the codon optimized SEQ ID NO: 2) was cloned into an expression vector under the control of a chicken-beta actin promoter with CMV enhancer, the promoter truncated by 390 nucleotides. A second copy of the native sequence of RdCVF (or the codon optimized SEQ ID NO: 2) was cloned into the same cassette under the control of a second copy of the same promoter. The expression construct was flanked by AAV2 ITRs thus forming the rAAV genome 2xRdCVF. The rAAV genome with native RdCVF sequences is reported in SEQ ID NO: 5. The rAAV genome with codon optimized sequences is reported as SEQ ID NO: 8. Either of these rAAV genomes was then inserted into a proviral plasmid, p617 (see International Patent Application Publication No. WO2012/158757A1), thereby generating the proviral plasmid SEQ ID NO: 6 (with native RdCVF) or the proviral plasmid p857 of SEQ ID NO: 9 (codon optimized RdCVF) which permits expression of two copies of the short RdCVF protein in a single vector.

The features of the rAAV genome 2xRdCVF containing the native sequences SEQ ID NO: 5) and the plasmid called pAAV.CMV.CBA.delta390.hRdCVFL.2x.synITR.long—native RdCVF (SEQ ID NO: 6) are described below in Table 2A, with reference to the nucleotide positions (Nts) in each sequence.

TABLE 2A SEQUENCES rAAV genome pAAV.CMV.CBA.delta- 2xRdCVF - 390.hRdCVF1.2x.- native synITR.long - sequence native sequences Nts Of Nts Of SEQ ID SEQ ID Sequence Feature NO: 5 NO: 6 Kan^(R) complement  9-100  9-803 B1 B2 T1 Txn Terminator —  988-1162 Complement pTR — 1063-1079 5 ITR (D segment) 117-246 1253-1382 (229-246) (1365-1382) Promoter Delta 390  307-1578 1443-2714 hRdCVF 1591-1935 2727-3071 Poly A 1940-2161 3076-3297 pTF3 complement 2337-2362 3473-3498 Bla Txn Terminator 2246-2546 3382-3682 Rpn Txn Terminator 2553-2666 3689-3802 Promoter 2697-3968 3833-5104 hRDCVF 3981-4325 5117-5461 Poly A 4330-4551 5466-5687 3′ ITR 4599-4728 5735-5864 BLA Txn Terminator — 5958-6258 pTF3 Complement — 6049-6074 Rpn Txn Terminator — 6265-6378 Lambda Stuffer —  6394-11460 pUC Ori Complement — 11621-12424

The features of the rAAV genome 2xRdCVF containing the codon optimized sequences of RdCVF (SEQ ID NO: 8) and p857opt plasmid called pAAV.CMV.CBA.delta390.hRdCVFL.2x.synITR.long (SEQ ID NO: 9) are described below in Table 2B, with reference to the nucleotide positions (Nts) in each sequence.

TABLE 2B p857opt SEQUENCES pAAV.CMV.CBA.delta- rAAV genome 390.hRdCVF1.2x.- cassette synITR.long Nts Of Nts Of SEQ ID SEQ ID Sequence Feature NO: 8 NO: 9 Kan^(R) complement  9-100  9-803 B1 B2 T1 Txn Terminator —  988-1162 Complement pTR — 1063-1079 5′ ITR (D segment) 117-246 1253-1382 (229-246) (1365-1382) Promoter Delta 390  307-1578 1443-2714 hoptRdCVF 1579-1926 2715-3062 Poly A 1931-2152 3067-3288 pTF3 complement 2328-2353 3464-3489 Bla Txn Terminator 2237-2537 3373-3673 Rpn Txn Terminator 2544-2657 3680-3793 Promoter 2688-3959 3824-5095 hoptRDCVF 3960-4307 5096-5443 Poly A 4312-4533 5448-5669 3′ ITR 4581-4710 5717-5846 BLA Txn Terminator — 5940-6240 pTF3 Complement — 6031-6056 Rpn Txn Terminator — 6247-6360 Lambda Stuffer —  6376-11442 pUC Ori Complement — 11603-12406

Example 5 Construction of rAAV Co-Expressing Two Copies of hRDCVF

The rAAV genome from the proviral plasmids of SEQ ID NO: 8 or SEQ ID NO: 9 is packaged in a selected AAV capsid by culturing a packaging cell carrying the plasmid in the presence of sufficient viral sequences to permit packaging of the AAV genome into an infectious AAV envelope or capsid. In one embodiment, a method for producing the rAAV involves packaging in a stable rep and cap expressing mammalian host packaging cell line (such as B-50 as described in International Patent Application Publication No. WO 99/15685) with the adenovirus E1, E2a, and E4ORF6 DNA. Iodixanol gradient purification is followed by heparin-sepharose agarose column chromatography. Vector titers are determined using an infectious center assay.

AAV.CMV.CBA.delta390.hRdCVF1.2x.synITR.long virus (native or codon optimized) preparations are prepared and suspended in a suitable excipient, such as 180 mM NaCl, 10 mM NaPi, pH7.3, containing 0.0001%-0.01% Pluronic F68 (PF68). The composition of the saline component ranges from 160 mM to 180 mM NaCl. Other buffers are useful in such compositions, including HEPEs, sodium bicarbonate, TRIS, or 0.9% NaCl solution.

Several preparations of the rAAV are combined to a desired total volume. In one embodiment, a total volume is 1.0 to 10⁵ ml containing either a dose of 2.3×10¹¹ infectious particles or viral genomes or a concentration of 2.3×10¹¹ infectious particles or viral genomes/ml. Contaminating helper adenovirus and native AAV, assayed by serial dilution cytopathic effect or infectious center assay, respectively are anticipated to be orders of magnitude lower than vector AAV.

In a similar manner an rAAV containing tandem expression of two copies of the long form of RdCVF (2xRdCVFL) and corresponding plasmid are generated.

Still other methods of producing such rAAV particles involve use of an insect cell packaging cell line, such as described in Smith et al, ref 11, cited below.

Example 6 In Vitro And In Vivo Tests

The suspension of rAAV particles described in Examples 1 through 5 are employed to transduce target cell cultures in vitro, such as in mice or chicken retinal cell cultures, at multiplicities of infection (MOI) ranging from 10³ to 10⁶ rAAV viral particles per cell. Survival counts of cone photoreceptors from such species are counted to demonstrate the efficacy of gene transfer. Other suitable techniques for determining efficacy in such in vitro models are RT-PCR, immunocytochemistry, immunohisto-chemistry, and Western blot analysis.

The rAAV particles are also employed to transduce cells of the murine or other mammalian (e.g., canine or feline) retina after administration by subretinal injection of 10¹¹-10¹³ viral particles or 10¹¹-10¹³ viral particles/ml buffer. Expression of both hRdCVFL and hRdCVF together in transduced cells or retinas or expression of two copies of hRdCVF is assessed by retinal and visual function. These functions may be examined in animals using one or more of the techniques: electroretinograms (ERGs) looking at rod and (especially) cone photoreceptor function, optokinetic nystagmus, pupillometry, water maze testing, light-dark preference histology (retinal thickness, rows of nuclei in the outer nuclear layer, immunofluorescence to document transgene expression, cone photoreceptor counting, staining of retinal sections with peanut agglutinin—which identifies cone photoreceptor sheaths). Additionally, sampling of anterior chamber fluid is used to document the presence of the RdCVF transgenic protein.

Example 7 Efficacy In Human Subjects

The rAAV particles are also employed to transduce cells of human subject's retina after administration by subretinal injection of 10¹⁰-10¹² GC or viral particles in a suspension in a suitable buffered carrier. Expression of both hRdCVFL and hRdCVF together in transduced cells or retinas or expression of two copies of hRdCVF is assessed by retinal and visual function.

These functions may be examined in humans using one or more of the techniques: electroretinograms (ERGs) looking at rod and cone photoreceptor function pupillometry visual acuity contrast sensitivity color vision testing visual field testing (Humphrey visual fields/Goldmann visual fields) perimetry mobility test (obstacle course) reading speed test. Other useful tests include functional magnetic resonance imaging (fMRI) full-field light sensitivity testing, retinal structure studies including optical coherence tomography, fundus photography, fundus autofluorescence, adaptive optics and scanning laser ophthalmoscopy.

Methods of use of these recombinant viruses are introduced into human subjects and evaluated by techniques, such as described in the examples described in published international applications WO2016/185037 and WO2016/185242, incorporated by reference herein.

Each and every patent, patent application, and publication, including websites cited throughout specification, as well as U.S. provisional patent application No. 62/275,006, are incorporated herein by reference. Similarly, the SEQ ID NOs which are referenced herein and which appear in the appended Sequence Listing are incorporated by reference. While the invention has been described with reference to particular embodiments, it will be appreciated that modifications can be made without departing from the spirit of the invention. Such modifications are intended to fall within the scope of the appended claims.

TABLE 3 (Sequence Listing Free Text) The following information is provided for sequences containing free text under numeric identifier <223>. SEQ ID NO: (containing free text) Free text under <223> 4 rAAV genome with ITRs flanking an expression cassette containing RdCVF sequences and promoters 4 AAV 5′ ITR 4 hRdCVF short form codon optimized 4 hRdCVFL long form codon optimized 4 AAV 3′ ITR 5 p857 rAAV genome with two copies of RdCVF and promoters 5 KanR complement 5 AAV 5′ ITR 5 human RdCVF native short form 5 pTF3 complement 5 human RdCVF native short form second copy 5 AAV 3′ ITR 6 Plasmid containing the p857 rAAV genome containing native 2xRdCVF 6 KanR complement 6 pTR 6 AAV 5 ITR 6 B1 B2 T1 Txn Terminator Complement 6 hRdCVF (native short form) 6 pTF3 complement 6 hRdCVF native short form second copy 6 AAV 3′ ITR 6 pTF3 Complement 6 Lambda Stuffer 6 pUC Ori Complement 7 Plasmid containing the rAAV genome of p853 7 KanR complement 7 B1 B2 T1 Txn Terminator Complement 7 pTR 7 AAV 5′ ITR 7 human hRdCVF short form optimized sequence 7 hRDCVFL optimized sequence long form 7 AAV 3′ ITR 7 pTF3 Complement 7 Lambda Stuffer 7 pUC Ori Complement 8 rAAV genome expressing two copies of human RdCVF codon optimized short form sequences 8 KanR complement 8 AAV 5′ ITR 8 human optimized RdCVF short form 8 pTF3 complement 8 human optimized RdCVF short form second copy 8 AAV 3′ ITR 9 plasmid expressing rAAV genome with two copies of optimized human RdCVF short form 9 KanR complement 9 pTF3 complement 9 B1 B2 T1 Txn Terminator Complement 9 pTR 9 5′ AAV ITR 9 human optimized RdCVF short form 9 human optimized RdCVF short form second copy 9 AAV 3′ ITR 9 pTF3 Complement 9 Lambda Stuffer 9 pUC Ori Complement

REFERENCES

-   1. U.S. Pat. No. 7,795,387 -   2. U.S. Pat. No. 8,114,849 -   3. U.S. Pat. No. 8,394,756 -   4. U.S. Pat. No. 8,518,695 -   5. U.S. Pat. No. 8,957,043 -   6. US Patent Appin Publication No. 2009062188A1 -   7. Natalia Caporale et al, July 2011, LiGluR Restores Visual     Responses in Rodent Models of Inherited Blindness, Mol. Therapy,     19(7):1212-1219 -   8. Kotin, R M, April 2011 Large-scale recombinant adeno-associated     virus production., Hu. Mol. Genet, 20(1): R1-R6 -   9. Byrne et al, January 2015, “Viral-mediated RdCVF and RdCVFL     expression protects cone and rod photoreceptors in retinal     degeneration”, J. Clin. Invest., 125(1):105-116 -   10. Maguire, A M et al., October 2009 Age-dependent effects of RPE65     gene therapy for Leber's congenital amaurosis: a phase 1     dose-escalation trial. Lancet, DOI:10.1016/S0140-6736(09)61836-5 -   11. Smith, R H et al, June 2009 A Simplified Baculovirus-AAV     Expression Vector System Coupled With One-step Affinity Purification     Yields High-titer rAAV Stocks From Insect Cells, Mol. Ther., 17(11):     1889-1896 -   12. Bennicelli J et al, March 2008 Reversal of Blindness in Animal     Models of Leber Congenital Amaurosis Using Optimized AAV2-mediated     Gene Transfer, Mol. Ther., 16(3):458-465 -   13. International Patent Application Publication No. WO2013/063383 -   14. International Patent Application Publication No. WO2016/185037 -   15. International Patent Application Publication No. WO2016/185242 

The invention claimed is:
 1. An expression cassette comprising one or more of: (a) the nucleic acid sequence set forth in SEQ ID NO: 1, (b) the nucleic acid sequence set forth in SEQ ID NO: 2, (c) the nucleic acid sequence set forth in SEQ ID NO: 1 and the nucleic acid sequence set forth in SEQ ID NO: 2; and (d) two copies of the nucleic acid sequence set forth in SEQ ID NO: 2, wherein the nucleic acid sequence set forth in SEQ ID NO: 1 encodes RdCVFL and the nucleic acid sequence set forth in SEQ ID NO: 2 encodes RdCVF.
 2. The expression cassette according to claim 1, wherein each nucleic acid sequence is operatively associated with an expression control sequence that directs expression in a host cell.
 3. A recombinant AAV (rAAV) vector, wherein said rAAV vector comprises AAV inverted terminal repeat sequences flanking the expression cassette of claim
 1. 4. A vector or plasmid comprising the expression cassette of claim
 1. 5. An rAAV vector comprising AAV inverted terminal repeat sequences and an expression cassette comprising at least one of the nucleic acid sequences set forth in SEQ ID NO: 1 or SEQ ID NO: 2 and expression control sequences that direct expression of said nucleic acid sequences in a host cell.
 6. The rAAV vector of claim 5, comprising a 5′ AAV ITR sequence, a first CMV/CBA promoter, a first nucleic acid sequence set forth in SEQ ID NO: 1 or 2, a first polyadenylation sequence, transcriptional terminator sequences a second CMV/CBA promoter, a second nucleic acid sequence set forth in SEQ ID NO: 1 or 2, a second polyadenylation sequence and a 3′ AAV ITR sequence.
 7. An isolated host cell comprising the expression cassette of claim
 1. 8. A composition comprising an engineered nucleic acid molecule for use in the treatment of an ocular disease comprising: (a) the nucleic acid sequence set forth in SEQ ID NO: 1, (b) the nucleic acid sequence set forth in SEQ ID NO: 2, (c) the nucleic acid sequence set forth in SEQ ID NO: 1 and the nucleic acid sequence set forth in SEQ ID NO: 2; or (d) two copies of the nucleic acid sequence set forth in SEQ ID NO: 1 or SEQ ID NO: 2, wherein each nucleic acid sequence is under the control of expression control sequences which direct expression of the encoded RdCVFL or RdCVF in ocular cells; and a carrier suitable for delivery to the eye of a subject.
 9. A composition comprising a pharmaceutically acceptable carrier suitable for delivery to the eye and the rAAV vector of claim
 5. 